If you extract chromatograms from both MS2 and MS1, and Skyline notices that MS2 chromatograms cover a shorter time range than the MS1, Skyline will truncate the MS1 chromatograms so they cover the same time range as the MS2.
The reason that Skyline does this is that it is the correct thing to do if you have a schedules MS2 method where you have told the mass spectrometer when to collect MS2 spectra for specific molecules.

One thing that you can do to prevent Skyline from doing this is to tell Skyline that your MS2 acquisition method is "DDA". You can set the Acquisition Method at "Settings > Transition Settings > Full Scan".
When the acquisition method is "DDA", Skyline will not truncate your MS1 chromatograms. Also, Skyline will treat all of your MS2 peak areas as "non-quantitative" and the MS2 chromatograms will be drawn as dotted lines on the chromatogram graph.

I was not able to open the .d file that you attached (SeeMS.exe give me the error "Important blocks missing from main BAF file.") When I look at the chromatograms in your Skyline document, it looks like they might have come from DDA, since those MS2 chromatograms have long straight lines indicating periods of time when the mass spectrometer did not acquire a MS2 spectrum which matched the precursor.
-- Nick